When you first create a new project, you are immediately brought to the "Save As" dialogue box. If you don't want Logic to copy your samples, then uncheck the option in the dialog box "Copy external samples to project file." This will prevent the copying/duplicate files etc.

However, there are some things to consider here prior to disabling the "Copy External Audio..." option.

Consistent Sample Rate and Bit Depth. If you're pulling samples from a variety of sources, there is a chance they will differ in terms of sample rate and bit depth. With "Copy External..." selected, Logic will automatically convert these samples to match the defined project specs. Good for consistency in your workflow. To add, placing a sample with a differing sample rate from the project will result in a very odd sounding audio sample...

Destructive Editing. If the sample has not been copied to your project file and you wish to perform destructive sample edits to the audio file via Logic's Sample Editor (ex. Reverse, Fade In, etc.), you may be blocked from doing so depending upon the permission the file has. To add, destructively editing an original file will of course, destroy the original sound unless you have a backup somewhere.

I'll be the first to admit that Logic's handling/management of external audio is first-class pain in the dick. In a perfect world it would match the lovely management of a DAW like Ableton, but I digress. What I do is keep all of my projects (and respective samples) on a separate external drive from my other external drive that contains only audio samples. I have found that this separation keeps things nice and organized and frees my hard drive(s) of unnecessary duplicates.